Well, that was easier than I thought. I wasn't even half-way through setting up the test case when the error popped up. It's not at the level of merging multiple runs as I expected, but in measuring the coverage of runs on the symlinks themselves. Here's your test case.:

File1
Name: main.pl
Content: print "hi\n"

File2
Name linkdir/main.pl
Content: symlink to File1

Run:
$ perl -MDevel::Cover main.pl
Devel::Cover 0.76: Collecting coverage data for branch, condition, sta
+tement, subroutine and time.
    Pod coverage is unavailable.  Please install Pod::Coverage from CP
+AN.
Selecting packages matching:
Ignoring packages matching:
    /Devel/Cover[./]
Ignoring packages in:
    .
    /usr/lib/perl5/5.10.0
    /usr/lib/perl5/vendor_perl
    /usr/lib/perl5/vendor_perl/5.10.0
    /usr/lib64/perl5/5.10.0/x86_64-linux-thread-multi
    /usr/lib64/perl5/vendor_perl/5.10.0/x86_64-linux-thread-multi
    /usr/local/lib64/perl5/site_perl/5.10.0/x86_64-linux-thread-multi
hi
Devel::Cover: Writing coverage database to /path/to/cover_db/runs/1311
+608639.28154
----------------------------------- ------ ------ ------ ------ ------
+ ------
File                                  stmt   bran   cond    sub   time
+  total
----------------------------------- ------ ------ ------ ------ ------
+ ------
main.pl                              100.0    n/a    n/a    n/a    n/a
+  100.0
Total                                100.0    0.0    0.0    0.0    n/a
+  100.0
----------------------------------- ------ ------ ------ ------ ------
+ ------


$ perl -MDevel::Cover linkdir/main.pl
Devel::Cover 0.76: Collecting coverage data for branch, condition, sta
+tement, subroutine and time.
    Pod coverage is unavailable.  Please install Pod::Coverage from CP
+AN.
Selecting packages matching:
Ignoring packages matching:
    /Devel/Cover[./]
Ignoring packages in:
    .
    /usr/lib/perl5/5.10.0
    /usr/lib/perl5/vendor_perl
    /usr/lib/perl5/vendor_perl/5.10.0
    /usr/lib64/perl5/5.10.0/x86_64-linux-thread-multi
    /usr/lib64/perl5/vendor_perl/5.10.0/x86_64-linux-thread-multi
    /usr/local/lib64/perl5/site_perl/5.10.0/x86_64-linux-thread-multi
hi
Devel::Cover: Writing coverage database to /path/to/cover_db/runs/1311
+608812.28180
----------------------------------- ------ ------ ------ ------ ------
+ ------
File                                  stmt   bran   cond    sub   time
+  total
----------------------------------- ------ ------ ------ ------ ------
+ ------
linkdir/main.pl                        n/a    n/a    n/a    n/a    n/a
+    n/a
Total                                  0.0    0.0    0.0    0.0    n/a
+    0.0
----------------------------------- ------ ------ ------ ------ ------
+ ------
[download]

The problem is measuring code coverage at all when running a symbolically linked script that is not in the current working director. I didn't show the results, but if you run the same symlinked script without running the 'main' non-linked path first, then it captures the coverage. When you run main.pl first, then run linkdir/main.pl next that's when you get the failure.

update: Forgot to mention that you don't get this error when the symlink is in the same directory as what it links to.